Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: XVK61

Calculation Name: 3GEF-A-Xray33

Preferred Name: Prelamin-A/C

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3GEF

Chain ID: A

ChEMBL ID: CHEMBL1293235

UniProt ID: P02545

Base Structure: X-ray

Registration Date: 2018-09-07

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 190
LigandCharge CSD=-1
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1115528.080567
FMO2-HF: Nuclear repulsion 1064177.903707
FMO2-HF: Total energy -51350.17686
FMO2-MP2: Total energy -51498.585773


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:435:SER)


Summations of interaction energy for fragment #1(A:435:SER)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-17.96-10.9951.452-4.281-4.137-0.026
Interaction energy analysis for fragmet #1(A:435:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : 0.015
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A437SER0-0.065-0.0573.797-0.8191.828-0.021-1.366-1.2600.008
4A438GLY0-0.047-0.0206.1710.1060.1060.0000.0000.0000.000
5A439ARG10.7770.8608.195-0.113-0.1130.0000.0000.0000.000
6A440VAL0-0.030-0.01311.3430.1180.1180.0000.0000.0000.000
7A441ALA0-0.0060.01312.334-0.178-0.1780.0000.0000.0000.000
8A442VAL00.0370.00614.9080.0430.0430.0000.0000.0000.000
9A443GLU-1-0.824-0.90617.528-0.236-0.2360.0000.0000.0000.000
10A444GLU-1-0.858-0.93520.451-0.205-0.2050.0000.0000.0000.000
11A445VAL0-0.048-0.02421.486-0.031-0.0310.0000.0000.0000.000
12A446ASP-1-0.781-0.86424.233-0.206-0.2060.0000.0000.0000.000
13A447GLU-1-0.819-0.92227.828-0.219-0.2190.0000.0000.0000.000
14A448GLU-1-0.940-0.96629.589-0.167-0.1670.0000.0000.0000.000
15A449GLY0-0.0180.00728.2800.0040.0040.0000.0000.0000.000
16A450LYS10.9600.96928.9990.1690.1690.0000.0000.0000.000
17A451PHE0-0.030-0.01825.842-0.007-0.0070.0000.0000.0000.000
18A452VAL00.0200.01920.088-0.011-0.0110.0000.0000.0000.000
19A453ARG10.8900.95722.6650.2480.2480.0000.0000.0000.000
20A454LEU0-0.031-0.01816.540-0.039-0.0390.0000.0000.0000.000
21A455ARG10.8530.90917.8890.2710.2710.0000.0000.0000.000
22A456ASN0-0.026-0.00215.665-0.073-0.0730.0000.0000.0000.000
23A457LYS10.9230.95112.8570.5190.5190.0000.0000.0000.000
24A458SER0-0.0050.00113.4360.0600.0600.0000.0000.0000.000
25A459ASN00.0330.00015.533-0.007-0.0070.0000.0000.0000.000
26A460GLU-1-0.800-0.89311.9760.4230.4230.0000.0000.0000.000
27A461ASP-1-0.799-0.89815.333-0.090-0.0900.0000.0000.0000.000
28A462GLN00.0090.02410.0850.0530.0530.0000.0000.0000.000
29A463SER0-0.049-0.03013.486-0.027-0.0270.0000.0000.0000.000
30A464MET0-0.013-0.02312.979-0.048-0.0480.0000.0000.0000.000
31A465GLY00.0350.03014.789-0.037-0.0370.0000.0000.0000.000
32A466ASN0-0.036-0.01714.819-0.049-0.0490.0000.0000.0000.000
33A467TRP00.0100.0329.875-0.236-0.2360.0000.0000.0000.000
34A468GLN0-0.008-0.04013.4220.2410.2410.0000.0000.0000.000
35A469ILE0-0.0170.00314.646-0.106-0.1060.0000.0000.0000.000
36A470LYS10.9110.97312.5181.2041.2040.0000.0000.0000.000
37A471ARG10.8430.91417.3740.3600.3600.0000.0000.0000.000
38A472GLN0-0.031-0.02719.805-0.016-0.0160.0000.0000.0000.000
39A473ASN00.009-0.00121.581-0.010-0.0100.0000.0000.0000.000
40A474GLY00.0410.01225.1600.0130.0130.0000.0000.0000.000
41A475ASP-1-0.913-0.94924.878-0.299-0.2990.0000.0000.0000.000
42A476ASP-1-0.888-0.91626.484-0.265-0.2650.0000.0000.0000.000
43A477PRO0-0.0090.00524.921-0.029-0.0290.0000.0000.0000.000
44A478LEU00.0090.01117.656-0.005-0.0050.0000.0000.0000.000
45A479LEU0-0.045-0.00121.8030.0200.0200.0000.0000.0000.000
46A480THR00.022-0.02717.743-0.079-0.0790.0000.0000.0000.000
47A481TYR0-0.0180.02619.4890.0730.0730.0000.0000.0000.000
48A482TRP00.0430.00715.822-0.096-0.0960.0000.0000.0000.000
49A483PHE00.0080.01116.7180.0670.0670.0000.0000.0000.000
50A484PRO00.0270.01519.3850.0000.0000.0000.0000.0000.000
51A485PRO00.0280.00319.191-0.020-0.0200.0000.0000.0000.000
52A486LYS10.9370.97018.9210.1380.1380.0000.0000.0000.000
53A487PHE00.0100.01818.3710.0400.0400.0000.0000.0000.000
54A488THR00.0440.01817.398-0.024-0.0240.0000.0000.0000.000
55A489LEU00.0080.03616.8120.0180.0180.0000.0000.0000.000
56A490LYS10.9070.94017.6020.0520.0520.0000.0000.0000.000
57A491ALA00.0260.02218.019-0.036-0.0360.0000.0000.0000.000
58A492GLY00.0550.03118.6780.0140.0140.0000.0000.0000.000
59A493GLN0-0.058-0.01120.547-0.013-0.0130.0000.0000.0000.000
60A494VAL00.0280.00520.500-0.037-0.0370.0000.0000.0000.000
61A495VAL0-0.0170.00520.0630.0210.0210.0000.0000.0000.000
62A496THR00.001-0.01322.497-0.036-0.0360.0000.0000.0000.000
63A497ILE0-0.068-0.01620.5710.0120.0120.0000.0000.0000.000
64A498TRP00.022-0.01624.520-0.013-0.0130.0000.0000.0000.000
65A499ALA00.0240.01627.869-0.008-0.0080.0000.0000.0000.000
66A500ALA0-0.036-0.02428.7520.0200.0200.0000.0000.0000.000
67A501GLY0-0.002-0.01031.4650.0150.0150.0000.0000.0000.000
68A502ALA0-0.0300.00131.6210.0090.0090.0000.0000.0000.000
69A503GLY0-0.029-0.00833.6770.0080.0080.0000.0000.0000.000
70A504ALA00.0210.03232.2410.0100.0100.0000.0000.0000.000
71A505THR0-0.011-0.00634.3430.0020.0020.0000.0000.0000.000
72A506HIS0-0.027-0.01930.110-0.011-0.0110.0000.0000.0000.000
73A507SER00.0290.00030.0300.0190.0190.0000.0000.0000.000
74A508PRO0-0.0280.02626.233-0.009-0.0090.0000.0000.0000.000
75A509PRO0-0.035-0.02823.6300.0150.0150.0000.0000.0000.000
76A510THR00.040-0.01224.283-0.023-0.0230.0000.0000.0000.000
77A511ASP-1-0.793-0.85026.239-0.207-0.2070.0000.0000.0000.000
78A512LEU0-0.046-0.02722.4920.0100.0100.0000.0000.0000.000
79A513VAL00.0600.04426.520-0.005-0.0050.0000.0000.0000.000
80A514TRP00.0020.00423.452-0.016-0.0160.0000.0000.0000.000
81A515LYS10.9260.94426.4680.2210.2210.0000.0000.0000.000
82A516ALA0-0.072-0.05028.270-0.011-0.0110.0000.0000.0000.000
83A517GLN00.0780.06726.388-0.003-0.0030.0000.0000.0000.000
84A518ASN00.009-0.01729.430-0.004-0.0040.0000.0000.0000.000
85A519THR00.0240.00829.9400.0040.0040.0000.0000.0000.000
86A520TRP0-0.021-0.01220.975-0.031-0.0310.0000.0000.0000.000
87A521GLY00.0000.00226.013-0.023-0.0230.0000.0000.0000.000
88A522CSD-1-0.904-0.93928.300-0.224-0.2240.0000.0000.0000.000
89A523GLY00.002-0.02030.2940.0000.0000.0000.0000.0000.000
90A524ASN00.012-0.01129.595-0.005-0.0050.0000.0000.0000.000
91A525SER0-0.018-0.01424.724-0.014-0.0140.0000.0000.0000.000
92A526LEU00.0410.04024.024-0.011-0.0110.0000.0000.0000.000
93A527ARG10.7610.85913.2130.8770.8770.0000.0000.0000.000
94A528THR00.005-0.01718.211-0.001-0.0010.0000.0000.0000.000
95A529ALA0-0.008-0.00413.116-0.002-0.0020.0000.0000.0000.000
96A530LEU00.0010.01212.1570.0920.0920.0000.0000.0000.000
97A531ILE0-0.033-0.0199.963-0.265-0.2650.0000.0000.0000.000
98A532ASN00.0610.0184.9911.0641.0640.0000.0000.0000.000
99A533SER00.0170.0039.522-0.023-0.0230.0000.0000.0000.000
100A534THR0-0.071-0.0266.395-0.063-0.0630.0000.0000.0000.000
101A535GLY00.0250.0128.8390.1490.1490.0000.0000.0000.000
102A536GLU-1-0.841-0.8762.539-21.782-18.1101.431-2.583-2.521-0.033
103A537GLU-1-0.824-0.8996.812-0.946-0.9460.0000.0000.0000.000
104A538VAL0-0.024-0.0155.848-0.557-0.5570.0000.0000.0000.000
105A539ALA0-0.0250.0028.0460.3300.3300.0000.0000.0000.000
106A540MET0-0.0010.01311.5290.0150.0150.0000.0000.0000.000
107A541ARG10.9080.95514.6980.4350.4350.0000.0000.0000.000
108A542LYS10.8840.94518.3320.3900.3900.0000.0000.0000.000
109A543LEU0-0.0090.00820.7210.0230.0230.0000.0000.0000.000
110A544VAL0-0.009-0.01224.009-0.009-0.0090.0000.0000.0000.000
111A545ARG10.9080.96126.6140.2030.2030.0000.0000.0000.000
112A546SER0-0.038-0.02930.363-0.001-0.0010.0000.0000.0000.000
113A547VAL00.0090.01827.791-0.001-0.0010.0000.0000.0000.000
114A548THR00.0070.00330.9770.0130.0130.0000.0000.0000.000
115A549VAL0-0.037-0.01029.742-0.011-0.0110.0000.0000.0000.000
116A550VAL0-0.001-0.00431.2920.0070.0070.0000.0000.0000.000
117A551GLU-1-0.980-1.00031.606-0.108-0.1080.0000.0000.0000.000
118A552ASP-2-1.841-1.87933.655-0.182-0.1820.0000.0000.0000.000
119A401HOH0-0.011-0.01120.8560.0040.0040.0000.0000.0000.000
120A405HOH0-0.032-0.03127.1670.0050.0050.0000.0000.0000.000
121A406HOH00.1210.1226.2010.0970.0970.0000.0000.0000.000
122A407HOH0-0.012-0.0119.4350.0680.0680.0000.0000.0000.000
123A410HOH0-0.004-0.0168.239-0.040-0.0400.0000.0000.0000.000
124A411HOH0-0.003-0.00725.922-0.009-0.0090.0000.0000.0000.000
125A412HOH00.002-0.01323.9930.0060.0060.0000.0000.0000.000
126A414HOH00.0030.00023.6450.0060.0060.0000.0000.0000.000
127A415HOH0-0.0020.00515.489-0.022-0.0220.0000.0000.0000.000
128A417HOH00.0100.01117.079-0.017-0.0170.0000.0000.0000.000
129A419HOH0-0.005-0.0159.439-0.029-0.0290.0000.0000.0000.000
130A420HOH00.0060.00722.3590.0020.0020.0000.0000.0000.000
131A428HOH0-0.014-0.01527.2160.0020.0020.0000.0000.0000.000
132A429HOH00.005-0.00317.121-0.020-0.0200.0000.0000.0000.000
133A431HOH00.0190.01834.314-0.004-0.0040.0000.0000.0000.000
134A432HOH00.000-0.0167.2880.0300.0300.0000.0000.0000.000
135A554HOH0-0.052-0.03236.2740.0010.0010.0000.0000.0000.000
136A556HOH0-0.019-0.02223.5310.0080.0080.0000.0000.0000.000
137A557HOH0-0.038-0.03729.0980.0070.0070.0000.0000.0000.000
138A558HOH00.0140.01626.476-0.006-0.0060.0000.0000.0000.000
139A559HOH0-0.071-0.0513.9320.7860.832-0.001-0.008-0.0380.000
140A560HOH0-0.088-0.0886.553-0.279-0.2790.0000.0000.0000.000
141A561HOH00.0140.01322.411-0.010-0.0100.0000.0000.0000.000
142A562HOH0-0.043-0.04319.6260.0100.0100.0000.0000.0000.000
143A563HOH0-0.025-0.00112.0620.0230.0230.0000.0000.0000.000
144A564HOH0-0.0070.01521.394-0.015-0.0150.0000.0000.0000.000
145A565HOH00.0320.02217.476-0.008-0.0080.0000.0000.0000.000
146A566HOH0-0.037-0.02823.6610.0020.0020.0000.0000.0000.000
147A567HOH00.0350.02830.194-0.007-0.0070.0000.0000.0000.000
148A568HOH00.0510.03131.680-0.006-0.0060.0000.0000.0000.000
149A569HOH00.0130.00226.4290.0080.0080.0000.0000.0000.000
150A570HOH0-0.063-0.05136.333-0.001-0.0010.0000.0000.0000.000
151A571HOH0-0.020-0.03131.7770.0000.0000.0000.0000.0000.000
152A572HOH0-0.030-0.02136.5680.0020.0020.0000.0000.0000.000
153A573HOH00.002-0.01531.8390.0030.0030.0000.0000.0000.000
154A574HOH00.0190.02112.865-0.050-0.0500.0000.0000.0000.000
155A576HOH0-0.036-0.01733.883-0.003-0.0030.0000.0000.0000.000
156A577HOH0-0.035-0.02820.663-0.007-0.0070.0000.0000.0000.000
157A578HOH0-0.075-0.04822.7710.0100.0100.0000.0000.0000.000
158A579HOH0-0.032-0.01427.463-0.004-0.0040.0000.0000.0000.000
159A583HOH0-0.009-0.00319.588-0.009-0.0090.0000.0000.0000.000
160A586HOH0-0.054-0.03622.106-0.003-0.0030.0000.0000.0000.000
161A587HOH00.0130.00823.215-0.011-0.0110.0000.0000.0000.000
162A590HOH00.0030.00630.385-0.001-0.0010.0000.0000.0000.000
163A591HOH0-0.045-0.02822.925-0.012-0.0120.0000.0000.0000.000
164A595HOH00.006-0.00128.579-0.004-0.0040.0000.0000.0000.000
165A596HOH0-0.013-0.02334.568-0.002-0.0020.0000.0000.0000.000
166A600HOH00.0050.00934.482-0.005-0.0050.0000.0000.0000.000
167A601HOH0-0.023-0.01718.905-0.018-0.0180.0000.0000.0000.000
168A602HOH00.0400.0237.1690.0860.0860.0000.0000.0000.000
169A603HOH00.0580.03132.685-0.004-0.0040.0000.0000.0000.000
170A606HOH00.0350.02024.027-0.015-0.0150.0000.0000.0000.000
171A624HOH00.0430.0315.572-0.425-0.4250.0000.0000.0000.000
172A625HOH00.0600.04124.686-0.011-0.0110.0000.0000.0000.000
173A629HOH0-0.018-0.01932.0490.0030.0030.0000.0000.0000.000
174A632HOH0-0.024-0.01436.5200.0020.0020.0000.0000.0000.000
175A645HOH0-0.028-0.01321.552-0.008-0.0080.0000.0000.0000.000
176A658HOH00.0260.02031.847-0.002-0.0020.0000.0000.0000.000
177A660HOH0-0.030-0.02318.824-0.030-0.0300.0000.0000.0000.000
178A662HOH00.0410.02818.9810.0110.0110.0000.0000.0000.000
179A673HOH0-0.004-0.0232.8422.1032.7030.043-0.324-0.318-0.001
180A674HOH0-0.015-0.02221.9660.0050.0050.0000.0000.0000.000
181A691HOH00.0150.00123.1750.0070.0070.0000.0000.0000.000
182A697HOH0-0.008-0.00516.818-0.024-0.0240.0000.0000.0000.000
183A709HOH0-0.037-0.01229.1200.0050.0050.0000.0000.0000.000
184B595HOH0-0.022-0.0219.9440.0850.0850.0000.0000.0000.000
185B616HOH00.0360.02414.3420.0030.0030.0000.0000.0000.000
186B713HOH0-0.016-0.01031.7750.0030.0030.0000.0000.0000.000
187C555HOH00.0130.02622.8240.0030.0030.0000.0000.0000.000
188C556HOH00.0320.01830.5380.0010.0010.0000.0000.0000.000
189C563HOH0-0.026-0.01829.265-0.005-0.0050.0000.0000.0000.000
190D638HOH0-0.002-0.02022.572-0.011-0.0110.0000.0000.0000.000